Title |
State-of the art methodologies dictate new standards for phylogenetic analysis
|
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Published in |
BMC Ecology and Evolution, August 2013
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DOI | 10.1186/1471-2148-13-161 |
Pubmed ID | |
Authors |
Maria Anisimova, David A Liberles, Hervé Philippe, Jim Provan, Tal Pupko, Arndt von Haeseler |
Abstract |
The intention of this editorial is to steer researchers through methodological choices in molecular evolution, drawing on the combined expertise of the authors. Our aim is not to review the most advanced methods for a specific task. Rather, we define several general guidelines to help with methodology choices at different stages of a typical phylogenetic 'pipeline'. We are not able to provide exhaustive citation of a literature that is vast and plentiful, but we point the reader to a set of classical textbooks that reflect the state-of-the-art. We do not wish to appear overly critical of outdated methodology but rather provide some practical guidance on the sort of issues which should be considered. We stress that a reported study should be well-motivated and evaluate a specific hypothesis or scientific question. However, a publishable study should not be merely a compilation of available sequences for a protein family of interest followed by some standard analyses, unless it specifically addresses a scientific hypothesis or question. The rapid pace at which sequence data accumulate quickly outdates such publications. Although clearly, discoveries stemming from data mining, reports of new tools and databases and review papers are also desirable. |
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Geographical breakdown
Country | Count | As % |
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United Kingdom | 4 | 11% |
Spain | 3 | 9% |
Indonesia | 1 | 3% |
Austria | 1 | 3% |
India | 1 | 3% |
Japan | 1 | 3% |
Colombia | 1 | 3% |
Sweden | 1 | 3% |
Other | 3 | 9% |
Unknown | 12 | 34% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 20 | 57% |
Members of the public | 12 | 34% |
Science communicators (journalists, bloggers, editors) | 2 | 6% |
Practitioners (doctors, other healthcare professionals) | 1 | 3% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 7 | 2% |
Germany | 6 | 2% |
Brazil | 4 | 1% |
United Kingdom | 3 | <1% |
Spain | 2 | <1% |
Norway | 1 | <1% |
Austria | 1 | <1% |
Italy | 1 | <1% |
France | 1 | <1% |
Other | 8 | 3% |
Unknown | 275 | 89% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 80 | 26% |
Researcher | 74 | 24% |
Student > Master | 30 | 10% |
Student > Bachelor | 29 | 9% |
Professor > Associate Professor | 24 | 8% |
Other | 49 | 16% |
Unknown | 23 | 7% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 188 | 61% |
Biochemistry, Genetics and Molecular Biology | 45 | 15% |
Computer Science | 10 | 3% |
Environmental Science | 7 | 2% |
Earth and Planetary Sciences | 5 | 2% |
Other | 18 | 6% |
Unknown | 36 | 12% |